Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3MGQ

Binding of Nickel ions to the Nucleosome Core Particle

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0030527	molecular_function	structural constituent of chromatin
A	0031492	molecular_function	nucleosomal DNA binding
A	0031507	biological_process	heterochromatin formation
A	0046982	molecular_function	protein heterodimerization activity
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0006334	biological_process	nucleosome assembly
B	0030527	molecular_function	structural constituent of chromatin
B	0031507	biological_process	heterochromatin formation
B	0046982	molecular_function	protein heterodimerization activity
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0030527	molecular_function	structural constituent of chromatin
C	0031507	biological_process	heterochromatin formation
C	0046982	molecular_function	protein heterodimerization activity
D	0000786	cellular_component	nucleosome
D	0002227	biological_process	innate immune response in mucosa
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005615	cellular_component	extracellular space
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0006325	biological_process	chromatin organization
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0031507	biological_process	heterochromatin formation
D	0046982	molecular_function	protein heterodimerization activity
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0030527	molecular_function	structural constituent of chromatin
E	0031492	molecular_function	nucleosomal DNA binding
E	0031507	biological_process	heterochromatin formation
E	0046982	molecular_function	protein heterodimerization activity
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0006334	biological_process	nucleosome assembly
F	0030527	molecular_function	structural constituent of chromatin
F	0031507	biological_process	heterochromatin formation
F	0046982	molecular_function	protein heterodimerization activity
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0030527	molecular_function	structural constituent of chromatin
G	0031507	biological_process	heterochromatin formation
G	0046982	molecular_function	protein heterodimerization activity
H	0000786	cellular_component	nucleosome
H	0002227	biological_process	innate immune response in mucosa
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005615	cellular_component	extracellular space
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0006325	biological_process	chromatin organization
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0031507	biological_process	heterochromatin formation
H	0046982	molecular_function	protein heterodimerization activity
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI E 136

Chain	Residue
D	VAL45
E	ASP77

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NI J 74

Chain	Residue
I	DG-28
I	DT67
J	DG27

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 74

Chain	Residue
I	DG61

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 75

Chain	Residue
I	DG-3

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 75

Chain	Residue
J	DG48

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 76

Chain	Residue
J	DG-3

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 77

Chain	Residue
J	DG61

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NI D 123

Chain	Residue
D	GLU102
D	HIS106
F	HIS18

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 76

Chain	Residue
I	DG48

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI H 123

Chain	Residue
H	HIS79

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI I 77

Chain	Residue
I	DA26
I	DG27

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 78

Chain	Residue
J	DG8

site_id	BC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 78

Chain	Residue
I	DG-56

site_id	BC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 79

Chain	Residue
J	DG-6

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NI H 124

Chain	Residue
H	GLU102
H	LYS105
H	HIS106

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI J 80

Chain	Residue
J	DA29
J	DG30

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 81

Chain	Residue
J	DG-56

site_id	BC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI D 124

Chain	Residue
D	HIS79

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NI I 80

Chain	Residue
I	DG-35
I	DG-34
I	NI86

site_id	CC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 82

Chain	Residue
J	DG5

site_id	CC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 81

Chain	Residue
I	DA29

site_id	CC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 83

Chain	Residue
J	DG71

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NI I 82

Chain	Residue
I	DG24
I	DG25
I	NI89

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI J 84

Chain	Residue
J	DG-35
J	DG-34

site_id	CC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI J 85

Chain	Residue
J	DG24
J	DG25

site_id	CC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 83

Chain	Residue
I	DG71

site_id	CC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI I 84

Chain	Residue
I	DG64
I	DG65

site_id	DC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 86

Chain	Residue
J	DA-70

site_id	DC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI H 125

Chain	Residue
H	HIS46

site_id	DC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 87

Chain	Residue
J	DG-34

site_id	DC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI J 88

Chain	Residue
I	DG-15
J	DG14

site_id	DC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 85

Chain	Residue
I	DG-6

site_id	DC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI I 86

Chain	Residue
I	DG-34
I	NI80

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NI I 87

Chain	Residue
I	DG58
I	DC59
I	NI91
J	DG-59

site_id	DC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI F 103

Chain	Residue
F	ASP24

site_id	DC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI A 136

Chain	Residue
A	ASP77

site_id	EC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 89

Chain	Residue
J	DA-19

site_id	EC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI J 90

Chain	Residue
J	DG52

site_id	EC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI C 120

Chain	Residue
C	ASP90

site_id	EC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI I 88

Chain	Residue
I	DG52

site_id	EC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI J 91

Chain	Residue
I	DC-30
J	DA-70

site_id	EC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NI G 120

Chain	Residue
G	ASP90

site_id	EC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NI I 89

Chain	Residue
I	DG24
I	DG25
I	NI82

site_id	EC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI I 91

Chain	Residue
I	DT57
I	NI87

site_id	EC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NI J 105

Chain	Residue
J	DG64
J	DG65

site_id	FC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL G 3145

Chain	Residue
G	GLY44
G	GLY46
G	ALA47
H	THR87
H	SER88

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL C 3146

Chain	Residue
C	GLY46
C	ALA47
D	THR87
D	SER88

site_id	FC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL A 3147

Chain	Residue
A	PRO121
A	LYS122

site_id	FC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL E 3148

Chain	Residue
E	PRO121
E	LYS122

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA21-VAL27

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
B	GLY14-HIS18

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
A	LYS14-LEU20

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG89-GLY111

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
A	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	5
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	4
Details	DNA binding: {}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)